Recent high-throughput multiplex genetic technologies have enabled orders- of-magnitude advances in our ability to assay gene expression and chromosomal regions. For example, high-throughput capillary electrophoresis (CE) instruments can generate 10,000 data traces per day. These advances are necessary for accelerating cancer research. However, this ability to rapidly generate data has far outstripped our capability to review, edit, and enter such data for downstream computer analysis. A key bottleneck now impeding research progress is the (computer-assisted) manual scoring of data. This proposal focuses on the automated scoring of such multiplex genetic data, including differential display, microsatellite, and SNP assays. We propose to adapt, develop and refine fragment analysis computer software for modem high-throughput DNA separation instruments. This software will automatically score multiplex data from both gene expression and chromosomal analysis experiments. It will be able to use data generated on diverse DNA sequencing instruments, and will run on all common computer hardware. Such automation should be useful in high-throughput settings, such as searching for cancer related genes, and (ultimately) in clinical testing. PROPOSED COMMERCIAL APPLICATIONS: Modern cancer genetics research and diagnostics mandate high-throughput data generation for rapid medical progress. However, current manual data editing methods have become a significant bottleneck. The automated scoring software developed in this proposed study would provide a commercial solution to eliminating that bottleneck in both the lab and the clinic.